In Russia, the recent discovery of the remains of the two missing Romanov children has pitted science against the church

In the spring of 1979, Avdonin told me, he and several fellow geologists, hoping to locate the remains, obtained permits to conduct scientific research in the area. The ruse worked, and they quickly came across a place marked by planks laid in the earth. “There was nobody else around,” he told me. “We took shovels and we started digging.”

Avdonin spied the first bones—“three skulls, with bullet holes. We took them out of the soil. And we covered the place where we were digging, to leave no traces.”

Avdonin said he kept the skulls while he tried to find someone who could conduct forensic tests on them. After a year without success, he said, “we put the skulls back in the grave, because it was too dangerous to keep them.” Had he and the other men been discovered, “we could have easily been put in prison, or just disappeared.”

The men vowed to keep their findings secret, and they did so for ten years. But in 1990, in the last days of the Soviet regime, Avdonin wrote to Boris Yeltsin, at the time the chairman of the Supreme Council of Russia. While serving as Communist Party boss in Sverdlovsk in 1977, Yeltsin had carried out a Politburo order to destroy the Ipatiev house. (A Russian Orthodox church has recently gone up on the site.) But since then Yeltsin had morphed into a democrat, and Avdonin now felt he could trust him. “I told him where the remains lay,” Avdonin told me. “And I asked him to help me bring them back to history.” Yeltsin wrote back, and the next year, investigators from the Sverdlovsk region’s prosecutor’s office, using Avdonin’s information, exhumed nine skeletons from a single, shallow grave.

The bones had been found. Now it was the job of the scientists to make them speak. The Russian government, and Peter Sarandinaki of the U.S.-based Search Foundation, which promotes forensic study of the Romanov remains, asked pre-eminent forensic experts to help identify the skeletons. They included Peter Gill of the Forensic Science Service in Birmingham, England, Pavel Ivanov of the Genetic Laboratory in Moscow and later Michael Coble of the Armed Forces DNA Identification Laboratory in Rockville, Maryland.

A human cell contains two genomes, or sets of genes: mitochondrial DNA, passed down by the mother, and nuclear DNA, inherited from both parents. Nuclear DNA, unique to each individual, provides the most powerful identification tool. But because only one set of nuclear DNA exists in a cell, it is often difficult to obtain an intact sample, particularly from aged sources. By contrast, mitochondrial DNA has hundreds to thousands of copies per cell; more of these molecules are likely to survive.

In this case, the scientists were fortunate: they succeeded in extracting nuclear DNA from all nine skeletons. They found striking similarities in five of them—enough to conclude that “the bones belonged to one family, and it looked like parents and three kids,” says Evgeny Rogaev, a Russian-born geneticist at the University of Massachusetts, who was brought into the investigation.

The scientists also compared mitochondrial DNA from the female adult skeleton, presumably Alexandra, with that of a living DNA donor: Britain’s Prince Philip, who shared a common maternal ancestor—Queen Victoria—with the czarina. It matched.

In 1994, Ivanov, the Moscow-based scientist, obtained permission from members of the Romanov family to exhume Georgy Romanov, the czar’s younger brother, from his grave in St. Petersburg. (Georgy had died suddenly in 1899, at age 28.) Ivanov found that Georgy’s mitochondrial DNA was consistent with that of the adult male skeletal remains. Both samples also showed evidence of an extremely rare genetic mutation known as heteroplasmy.

The evidence led the forensic experts to one conclusion: the bones were those of Nicholas II, Alexandra and three of their five children. “The DNA testing was clear and convincing,” Coble says.